LAMMPS (4 Nov 2022)
# 20 styrene molecules
# three reactions defined

units real

boundary p p p

atom_style full

kspace_style pppm 1.0e-4

pair_style lj/class2/coul/long 8.5

angle_style class2

bond_style class2

dihedral_style class2

improper_style class2

variable T equal 530

read_data tiny_polystyrene.data    extra/bond/per/atom 5   extra/angle/per/atom 15   extra/dihedral/per/atom 15   extra/improper/per/atom 25   extra/special/per/atom 25
Reading data file ...
  orthogonal box = (1.7426663 1.7426663 1.7426663) to (18.257334 18.257334 18.257334)
  1 by 2 by 2 MPI processor grid
  reading atom labelmap ...
  reading bond labelmap ...
  reading angle labelmap ...
  reading dihedral labelmap ...
  reading improper labelmap ...
  reading atoms ...
  320 atoms
  reading velocities ...
  320 velocities
  scanning bonds ...
  8 = max bonds/atom
  scanning angles ...
  18 = max angles/atom
  scanning dihedrals ...
  22 = max dihedrals/atom
  scanning impropers ...
  26 = max impropers/atom
  reading bonds ...
  320 bonds
  reading angles ...
  480 angles
  reading dihedrals ...
  640 dihedrals
  reading impropers ...
  160 impropers
Finding 1-2 1-3 1-4 neighbors ...
  special bond factors lj:    0        0        0       
  special bond factors coul:  0        0        0       
     3 = max # of 1-2 neighbors
     6 = max # of 1-3 neighbors
    12 = max # of 1-4 neighbors
    39 = max # of special neighbors
  special bonds CPU = 0.001 seconds
  read_data CPU = 0.018 seconds

molecule mol1 2styrene_unreacted.molecule_template
Read molecule template mol1:
  1 molecules
  0 fragments
  32 atoms with max type 4
  32 bonds with max type 11
  48 angles with max type 19
  64 dihedrals with max type 21
  16 impropers with max type 8
molecule mol2 2styrene_reacted.molecule_template
Read molecule template mol2:
  1 molecules
  0 fragments
  32 atoms with max type 6
  33 bonds with max type 13
  54 angles with max type 22
  79 dihedrals with max type 19
  14 impropers with max type 7
molecule mol3 chain_plus_styrene_unreacted.molecule_template
Read molecule template mol3:
  1 molecules
  0 fragments
  46 atoms with max type 6
  47 bonds with max type 13
  75 angles with max type 22
  105 dihedrals with max type 21
  21 impropers with max type 8
molecule mol4 chain_plus_styrene_reacted.molecule_template
Read molecule template mol4:
  1 molecules
  0 fragments
  46 atoms with max type 6
  48 bonds with max type 13
  81 angles with max type 22
  121 dihedrals with max type 19
  19 impropers with max type 7
molecule mol5 chain_chain_unreacted.molecule_template
Read molecule template mol5:
  1 molecules
  0 fragments
  50 atoms with max type 6
  51 bonds with max type 13
  84 angles with max type 22
  118 dihedrals with max type 19
  20 impropers with max type 7
molecule mol6 chain_chain_reacted.molecule_template
Read molecule template mol6:
  1 molecules
  0 fragments
  50 atoms with max type 6
  52 bonds with max type 13
  90 angles with max type 22
  135 dihedrals with max type 19
  18 impropers with max type 2

thermo 100

# dump 1 all xyz 5 test_vis.xyz

fix rxn1 all bond/react stabilization yes statted_grp .03  react rxn1 all 1 0 3.0 mol1 mol2 2styrene_map stabilize_steps 100  react rxn2 all 1 0 3.0 mol3 mol4 chain_plus_styrene_map stabilize_steps 100  react rxn3 all 1 0 5.0 mol5 mol6 chain_chain_map stabilize_steps 100
dynamic group bond_react_MASTER_group defined
dynamic group statted_grp_REACT defined

fix 1 statted_grp_REACT nvt temp $T $T 100
fix 1 statted_grp_REACT nvt temp 530 $T 100
fix 1 statted_grp_REACT nvt temp 530 530 100

fix 4 bond_react_MASTER_group temp/rescale 1 $T $T 1 1
fix 4 bond_react_MASTER_group temp/rescale 1 530 $T 1 1
fix 4 bond_react_MASTER_group temp/rescale 1 530 530 1 1

thermo_style custom step temp press density f_rxn1[1] f_rxn1[2] f_rxn1[3]

run 10000

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

Your simulation uses code contributions which should be cited:

- fix bond/react: reacter.org doi:10.1016/j.polymer.2017.09.038, doi:10.1021/acs.macromol.0c02012

@Article{Gissinger17,
 author = {J. R. Gissinger and B. D. Jensen and K. E. Wise},
 title = {Modeling Chemical Reactions in Classical Molecular Dynamics Simulations},
 journal = {Polymer},
 year =    2017,
 volume =  128,
 pages =   {211--217}
}

@Article{Gissinger20,
 author = {J. R. Gissinger, B. D. Jensen, K. E. Wise},
 title = {{REACTER}: A Heuristic Method for Reactive Molecular Dynamics},
 journal = {Macromolecules},
 year =    2020,
 volume =  53,
 number =  22,
 pages =   {9953--9961}
}

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

PPPM initialization ...
WARNING: System is not charge neutral, net charge = -0.004 (../kspace.cpp:327)
  using 12-bit tables for long-range coulomb (../kspace.cpp:342)
  G vector (1/distance) = 0.25561147
  grid = 6 6 6
  stencil order = 5
  estimated absolute RMS force accuracy = 0.0097469157
  estimated relative force accuracy = 2.9352547e-05
  using double precision KISS FFT
  3d grid and FFT values/proc = 704 72
Generated 21 of 21 mixed pair_coeff terms from sixthpower/geometric mixing rule
Neighbor list info ...
  update: every = 1 steps, delay = 0 steps, check = yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 10.5
  ghost atom cutoff = 10.5
  binsize = 5.25, bins = 4 4 4
  2 neighbor lists, perpetual/occasional/extra = 1 1 0
  (1) pair lj/class2/coul/long, perpetual
      attributes: half, newton on
      pair build: half/bin/newton
      stencil: half/bin/3d
      bin: standard
  (2) fix bond/react, occasional, copy from (1)
      attributes: half, newton on
      pair build: copy
      stencil: none
      bin: none
Per MPI rank memory allocation (min/avg/max) = 31.03 | 31.05 | 31.06 Mbytes
   Step          Temp          Press         Density       f_rxn1[1]      f_rxn1[2]      f_rxn1[3]   
         0   320.13638     -376.0844       0.76796752     0              0              0            
       100   342.22237     -3489.4495      0.76796752     0              0              0            
       200   412.23828     -1367.104       0.76796752     0              0              0            
       300   467.98145      4841.002       0.76796752     0              0              0            
       400   505.39864      2213.0509      0.76796752     1              0              0            
       500   519.63371     -28223.513      0.76796752     2              0              0            
       600   526.40655      8701.2728      0.76796752     2              0              0            
       700   579.91953      2507.5868      0.76796752     2              0              0            
       800   517.29593      5558.2895      0.76796752     2              0              0            
       900   503.38392     -5027.1154      0.76796752     2              0              0            
      1000   509.30767      3979.0529      0.76796752     2              0              0            
      1100   551.34763      5119.0848      0.76796752     2              0              0            
      1200   562.5176      -2867.8688      0.76796752     2              0              0            
      1300   552.90918      2090.7508      0.76796752     2              0              0            
      1400   516.10716      3374.2169      0.76796752     2              0              0            
      1500   518.70418      471.99711      0.76796752     2              0              0            
      1600   559.49915      5450.8774      0.76796752     2              0              0            
      1700   531.50638      4525.5892      0.76796752     2              0              0            
      1800   529.18331     -3566.9245      0.76796752     2              0              0            
      1900   517.79846     -2364.8287      0.76796752     2              0              0            
      2000   495.0983      -488.99696      0.76796752     2              0              0            
      2100   567.80521      2050.9596      0.76796752     3              0              0            
      2200   553.24434      5665.0753      0.76796752     3              0              0            
      2300   561.08278      2879.1572      0.76796752     3              0              0            
      2400   461.3712       3185.6091      0.76796752     3              0              0            
      2500   500.95595      565.81792      0.76796752     4              0              0            
      2600   538.3865       463.58228      0.76796752     4              0              0            
      2700   525.95739      2011.1914      0.76796752     4              0              0            
      2800   533.4197       157.38106      0.76796752     4              0              0            
      2900   526.27036      1331.5115      0.76796752     5              1              0            
      3000   502.65015     -93.915921      0.76796752     5              1              0            
      3100   505.4224      -1314.224       0.76796752     5              1              0            
      3200   538.52692      10420.644      0.76796752     5              1              0            
      3300   518.32801      5933.553       0.76796752     5              2              0            
      3400   540.04815      741.54438      0.76796752     6              2              1            
      3500   554.07567      5778.8913      0.76796752     6              2              1            
      3600   546.90828      4751.5437      0.76796752     6              2              1            
      3700   529.75739      432.20829      0.76796752     6              2              1            
      3800   542.806       -380.00399      0.76796752     6              2              1            
      3900   521.55789     -1224.1912      0.76796752     6              2              2            
      4000   519.73935      2792.996       0.76796752     6              2              2            
      4100   535.06314     -1926.8692      0.76796752     6              2              2            
      4200   549.75482      2852.5521      0.76796752     6              2              2            
      4300   510.71949      6581.1729      0.76796752     7              2              2            
      4400   485.93403     -695.24007      0.76796752     7              2              2            
      4500   535.3677       2519.2711      0.76796752     7              2              2            
      4600   504.87216      533.16619      0.76796752     7              2              2            
      4700   495.68939      5502.1672      0.76796752     7              2              2            
      4800   534.13893     -1187.1228      0.76796752     7              2              2            
      4900   512.56394      1731.3856      0.76796752     7              2              2            
      5000   508.63054      2467.0387      0.76796752     7              2              2            
      5100   501.65027      3403.8111      0.76796752     7              2              2            
      5200   556.68281      4310.0492      0.76796752     7              2              2            
      5300   506.86652     -773630.77      0.76796752     7              2              3            
      5400   570.01783      11663.867      0.76796752     7              2              3            
      5500   538.08785      6391.6546      0.76796752     7              2              3            
      5600   502.48456      44.409604      0.76796752     7              2              3            
      5700   545.75445      1558.6373      0.76796752     7              2              3            
      5800   517.5076      -166.52488      0.76796752     7              2              3            
      5900   558.64383      1528.1198      0.76796752     7              2              3            
      6000   557.8358       442.21273      0.76796752     7              2              3            
      6100   483.13771      5201.4489      0.76796752     8              2              3            
      6200   533.42675      5112.0828      0.76796752     8              2              3            
      6300   576.32772      269.77058      0.76796752     8              2              3            
      6400   492.79331      565.35222      0.76796752     8              2              4            
      6500   514.5727       6233.7568      0.76796752     8              2              4            
      6600   509.86906     -943.58621      0.76796752     8              2              4            
      6700   546.62752     -323284.04      0.76796752     8              2              5            
      6800   541.19749      1306.3182      0.76796752     8              2              5            
      6900   497.72333     -1792.483       0.76796752     8              2              5            
      7000   516.02636      2028.3813      0.76796752     8              2              5            
      7100   486.54013      6153.9142      0.76796752     8              2              5            
      7200   553.33698      4352.3987      0.76796752     8              2              5            
      7300   519.23896      6536.766       0.76796752     8              2              5            
      7400   486.74787     -1744.8351      0.76796752     8              2              5            
      7500   516.71935     -315.43649      0.76796752     8              2              5            
      7600   513.62572     -1100.1363      0.76796752     8              2              5            
      7700   531.11296      1727.7113      0.76796752     8              2              5            
      7800   530.82809      9566.2386      0.76796752     8              2              5            
      7900   513.09884      8545.6728      0.76796752     8              2              5            
      8000   511.38714      2995.8438      0.76796752     8              2              5            
      8100   527.76731      709.63649      0.76796752     8              2              5            
      8200   514.09092      2103.8591      0.76796752     8              2              5            
      8300   534.90612      7707.3378      0.76796752     8              2              5            
      8400   547.40716      660.54641      0.76796752     8              2              5            
      8500   518.75522     -872.69754      0.76796752     8              2              5            
      8600   511.70922      6645.6264      0.76796752     8              2              5            
      8700   480.70739     -640.57939      0.76796752     8              2              5            
      8800   527.35475      6944.8472      0.76796752     8              2              5            
      8900   554.26477     -2311.6153      0.76796752     8              2              5            
      9000   520.48502      1469.4805      0.76796752     8              2              5            
      9100   522.0619      -4159.697       0.76796752     8              2              5            
      9200   501.34664      7486.8266      0.76796752     8              2              5            
      9300   524.96422      6158.2524      0.76796752     8              2              5            
      9400   564.30456     -2964.7187      0.76796752     8              2              6            
      9500   569.02736      5765.8856      0.76796752     8              2              6            
      9600   554.31532      2805.5671      0.76796752     8              2              6            
      9700   521.3957      -924.74562      0.76796752     8              2              6            
      9800   518.45356     -2440.5266      0.76796752     8              2              6            
      9900   512.03787     -834.07647      0.76796752     8              2              6            
     10000   573.10576      4372.5769      0.76796752     8              2              6            
Loop time of 11.2088 on 4 procs for 10000 steps with 320 atoms

Performance: 77.082 ns/day, 0.311 hours/ns, 892.155 timesteps/s, 285.490 katom-step/s
100.0% CPU use with 4 MPI tasks x no OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 2.6217     | 2.8126     | 3.0128     |   9.5 | 25.09
Bond    | 2.0439     | 2.1734     | 2.3326     |   7.0 | 19.39
Kspace  | 1.4277     | 1.7772     | 2.0148     |  17.9 | 15.86
Neigh   | 0.32002    | 0.3201     | 0.3202     |   0.0 |  2.86
Comm    | 0.42382    | 0.43347    | 0.4412     |   1.1 |  3.87
Output  | 0.0013461  | 0.0015202  | 0.0020328  |   0.8 |  0.01
Modify  | 3.6386     | 3.6396     | 3.6408     |   0.0 | 32.47
Other   |            | 0.05092    |            |       |  0.45

Nlocal:             80 ave          93 max          71 min
Histogram: 1 1 0 0 1 0 0 0 0 1
Nghost:        2184.75 ave        2276 max        2092 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Neighs:        13678.5 ave       15576 max       11682 min
Histogram: 1 0 0 1 0 0 0 1 0 1

Total # of neighbors = 54714
Ave neighs/atom = 170.98125
Ave special neighs/atom = 10.9125
Neighbor list builds = 471
Dangerous builds = 0

# write_restart restart_longrun nofix
# write_data restart_longrun.data
Total wall time: 0:00:11
